Multiple sequence alignment - TraesCS5A01G386800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G386800 chr5A 100.000 6804 0 0 1 6804 584448643 584455446 0.000000e+00 12565.0
1 TraesCS5A01G386800 chr5A 85.068 221 31 2 592 810 559787423 559787643 2.470000e-54 224.0
2 TraesCS5A01G386800 chr5A 82.192 219 32 5 595 809 611475689 611475904 1.510000e-41 182.0
3 TraesCS5A01G386800 chr5A 96.000 50 2 0 178 227 705906126 705906175 1.570000e-11 82.4
4 TraesCS5A01G386800 chr5D 93.208 4888 213 60 1966 6804 464067604 464072421 0.000000e+00 7077.0
5 TraesCS5A01G386800 chr5D 90.062 1942 124 34 1 1911 464065707 464067610 0.000000e+00 2453.0
6 TraesCS5A01G386800 chr5D 82.648 219 34 4 595 811 438091916 438091700 2.500000e-44 191.0
7 TraesCS5A01G386800 chr5D 97.872 47 1 0 181 227 555061011 555061057 1.570000e-11 82.4
8 TraesCS5A01G386800 chr5B 92.249 4167 238 39 554 4692 570923629 570927738 0.000000e+00 5827.0
9 TraesCS5A01G386800 chr5B 91.948 1987 111 23 4844 6804 570928124 570930087 0.000000e+00 2737.0
10 TraesCS5A01G386800 chr5B 87.245 588 39 19 1 557 570905558 570906140 7.440000e-179 638.0
11 TraesCS5A01G386800 chr5B 85.340 191 14 11 4769 4955 320413653 320413833 1.170000e-42 185.0
12 TraesCS5A01G386800 chr5B 85.561 187 15 10 4776 4960 682169464 682169288 1.170000e-42 185.0
13 TraesCS5A01G386800 chr5B 96.000 50 2 0 178 227 103463318 103463367 1.570000e-11 82.4
14 TraesCS5A01G386800 chr6B 84.018 219 33 2 592 808 40071509 40071727 6.910000e-50 209.0
15 TraesCS5A01G386800 chr6B 86.264 182 14 9 4779 4958 358303033 358303205 3.240000e-43 187.0
16 TraesCS5A01G386800 chr6B 86.264 182 13 10 4779 4959 460505230 460505400 3.240000e-43 187.0
17 TraesCS5A01G386800 chr3A 84.058 207 31 2 597 801 670673989 670674195 1.500000e-46 198.0
18 TraesCS5A01G386800 chr3A 87.013 77 9 1 228 303 560130670 560130746 1.220000e-12 86.1
19 TraesCS5A01G386800 chr2D 83.256 215 31 5 597 808 160597397 160597609 6.960000e-45 193.0
20 TraesCS5A01G386800 chr2D 88.235 85 6 1 5262 5342 425742569 425742653 1.560000e-16 99.0
21 TraesCS5A01G386800 chr2D 89.474 76 6 2 228 301 644517568 644517643 2.020000e-15 95.3
22 TraesCS5A01G386800 chr2D 87.013 77 9 1 228 303 382384157 382384081 1.220000e-12 86.1
23 TraesCS5A01G386800 chr2D 96.000 50 2 0 178 227 193393251 193393202 1.570000e-11 82.4
24 TraesCS5A01G386800 chr1A 82.870 216 31 6 597 808 578473038 578473251 9.010000e-44 189.0
25 TraesCS5A01G386800 chr7A 85.417 192 14 10 4761 4947 48816419 48816601 3.240000e-43 187.0
26 TraesCS5A01G386800 chr7A 94.118 51 2 1 171 221 595198167 595198216 7.320000e-10 76.8
27 TraesCS5A01G386800 chr3B 85.946 185 14 10 4779 4961 2885353 2885179 3.240000e-43 187.0
28 TraesCS5A01G386800 chr3B 86.598 97 7 4 185 277 10286801 10286707 1.210000e-17 102.0
29 TraesCS5A01G386800 chr3B 86.905 84 8 2 5261 5341 194074855 194074772 2.610000e-14 91.6
30 TraesCS5A01G386800 chr3B 84.375 96 10 4 217 307 438579043 438579138 9.400000e-14 89.8
31 TraesCS5A01G386800 chr3B 100.000 28 0 0 544 571 705917048 705917075 1.200000e-02 52.8
32 TraesCS5A01G386800 chr2B 85.870 184 14 10 4779 4961 314771398 314771570 1.170000e-42 185.0
33 TraesCS5A01G386800 chr2B 96.774 31 1 0 544 574 104255282 104255252 1.200000e-02 52.8
34 TraesCS5A01G386800 chr3D 89.286 84 6 2 5260 5341 250931575 250931493 1.210000e-17 102.0
35 TraesCS5A01G386800 chr3D 84.884 86 10 3 224 307 549066864 549066948 4.370000e-12 84.2
36 TraesCS5A01G386800 chr6A 88.889 81 4 2 5262 5341 301951288 301951364 2.020000e-15 95.3
37 TraesCS5A01G386800 chr2A 87.805 82 8 2 228 307 769625600 769625681 2.020000e-15 95.3
38 TraesCS5A01G386800 chr6D 86.207 87 8 3 5255 5341 211444027 211443945 2.610000e-14 91.6
39 TraesCS5A01G386800 chr6D 97.872 47 1 0 181 227 323050184 323050138 1.570000e-11 82.4
40 TraesCS5A01G386800 chr6D 97.222 36 0 1 547 581 292299456 292299421 7.370000e-05 60.2
41 TraesCS5A01G386800 chr1D 87.059 85 6 4 5262 5341 279101376 279101460 2.610000e-14 91.6
42 TraesCS5A01G386800 chr1D 100.000 29 0 0 547 575 37220060 37220088 3.000000e-03 54.7
43 TraesCS5A01G386800 chr1B 86.905 84 8 3 5262 5343 539869528 539869610 2.610000e-14 91.6
44 TraesCS5A01G386800 chr4B 100.000 28 0 0 548 575 668813811 668813838 1.200000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G386800 chr5A 584448643 584455446 6803 False 12565 12565 100.0000 1 6804 1 chr5A.!!$F2 6803
1 TraesCS5A01G386800 chr5D 464065707 464072421 6714 False 4765 7077 91.6350 1 6804 2 chr5D.!!$F2 6803
2 TraesCS5A01G386800 chr5B 570923629 570930087 6458 False 4282 5827 92.0985 554 6804 2 chr5B.!!$F4 6250
3 TraesCS5A01G386800 chr5B 570905558 570906140 582 False 638 638 87.2450 1 557 1 chr5B.!!$F3 556


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
897 934 0.179040 GATGGGGATTACGGGCGAAA 60.179 55.000 0.0 0.0 0.00 3.46 F
1666 1709 1.135603 CCAAACGTGGTGCATGATGAG 60.136 52.381 0.0 0.0 40.42 2.90 F
2070 2129 0.103937 GCTAGTGCCTACTGCCTCTG 59.896 60.000 0.0 0.0 40.16 3.35 F
3829 3895 0.042131 ACCAATACCTCCCCTCACGA 59.958 55.000 0.0 0.0 0.00 4.35 F
4785 4874 0.034089 GAACATGGGGGAAGGACAGG 60.034 60.000 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1757 1.444383 CGTGCAGAGACTAAGCGCA 60.444 57.895 11.47 0.0 38.61 6.09 R
3128 3188 1.469079 GCAAATGCATGTACCGGGAAC 60.469 52.381 6.32 4.0 41.59 3.62 R
3944 4010 0.045008 TGATAGGCCACAGGGGGTAA 59.955 55.000 5.01 0.0 37.04 2.85 R
4918 5237 0.321671 GTGCTAGAAGCTCCCACACA 59.678 55.000 0.00 0.0 42.97 3.72 R
6540 6902 0.187851 CCCCCGGACTACTACTCCAT 59.812 60.000 0.73 0.0 0.00 3.41 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)



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AutoCloner maintained by Alex Coulton.